Complier issue with Linux RHEL 8

[modenab]

Hi -

I have a new RHEL 8 machine. While attempting to compile using "make" I get the following error messages. My search into the issue suggests it might be an issue with a mismatch in compilers. I am using the g++, as shown below.

Thank you,
Brian Modena

[modenab@localhost Nimbus]$ sudo make
make -C cplusplus/trim
make[1]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/trim'
mkdir -p bin/
g++ build/adapter_trim.o -g -L/usr/lib64 -std=c++0x -pthread
-Irwwb
-Iinclude
-lboost_program_options
-o bin/nimbus_trim
make[1]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/trim'
make -C cplusplus/align
make[1]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align'
make -C lib/libnimbus
make[2]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align/lib/libnimbus'
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AdapterTrim.cpp -o build/AdapterTrim.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Amplicon.cpp -o build/Amplicon.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Utils.cpp -o build/Utils.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/SAMrecord.cpp -o build/SAMrecord.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Read.cpp -o build/Read.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AmpliconIndex.cpp -o build/AmpliconIndex.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AmpliconAlignment.cpp -o build/AmpliconAlignment.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Alignment.cpp -o build/Alignment.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/_DNANode.cpp -o build/_DNANode.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/stdafx.cpp -o build/stdafx.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/io.cpp -o build/io.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AlignmentBuilder.cpp -o build/AlignmentBuilder.o
src/AlignmentBuilder.cpp: In member function ‘void Nimbus::AlnSet::delete_content()’:
src/AlignmentBuilder.cpp:40:36: warning: deleting object of polymorphic class type ‘Nimbus::alignment::Alignment’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
if( f_alignment != NULL ) delete f_alignment ;
^~~~~~~~~~~
src/AlignmentBuilder.cpp:41:36: warning: deleting object of polymorphic class type ‘Nimbus::alignment::Alignment’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
if( r_alignment != NULL ) delete r_alignment ;
^~~~~~~~~~~
ar -cvq libnimbus.a build/AdapterTrim.o build/Amplicon.o build/Utils.o build/SAMrecord.o build/Read.o build/AmpliconIndex.o build/AmpliconAlignment.o build/Alignment.o build/_DNANode.o build/stdafx.o build/io.o build/AlignmentBuilder.o
a - build/AdapterTrim.o
a - build/Amplicon.o
a - build/Utils.o
a - build/SAMrecord.o
a - build/Read.o
a - build/AmpliconIndex.o
a - build/AmpliconAlignment.o
a - build/Alignment.o
a - build/_DNANode.o
a - build/stdafx.o
a - build/io.o
a - build/AlignmentBuilder.o
rm -r build
make[2]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align/lib/libnimbus'
make -C lib/libthreadutils
make[2]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align/lib/libthreadutils'
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/TQueue.cpp -o build/TQueue.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/stdafx.cpp -o build/stdafx.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Signal.cpp -o build/Signal.o
ar -cvq libthreadutils.a build/TQueue.o build/stdafx.o build/Signal.o
a - build/TQueue.o
a - build/stdafx.o
a - build/Signal.o
rm -r build
make[2]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align/lib/libthreadutils'
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/preprocess.cpp -o build/preprocess.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/Worker.cpp -o build/Worker.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/Reader.cpp -o build/Reader.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/nimbus.cpp -o build/nimbus.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/nimbusheader.cpp -o build/nimbusheader.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/Writer.cpp -o build/Writer.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/opt.cpp -o build/opt.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/Manager.cpp -o build/Manager.o
mkdir -p build
g++ -c -g -Wall -O4 -std=c++0x -Iinclude
-Ilib/libnimbus/include
-Ilib/libthreadutils/include
-pthread src/main.cpp -o build/main.o
mkdir -p bin/
g++ build/preprocess.o build/Worker.o build/Reader.o build/nimbus.o build/nimbusheader.o build/Writer.o build/opt.o build/Manager.o build/main.o -g -L/usr/lib64 -std=c++0x -pthread
-Iinclude
-Llib/libnimbus -lnimbus -Ilib/libnimbus/include
-Llib/libthreadutils -lthreadutils -Ilib/libthreadutils/include
-o bin/nimbus_align
rm -r build
make[1]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align'
make -C cplusplus/call
make[1]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/call'
mkdir -p bin/
g++ build/call.o build/read_provider.o build/alignment_functions.o build/mpileup.o build/aspects.o build/refsequence.o build/main.o build/sample.o build/cigar.o -g -L/usr/lib64 -std=c++0x
-pthread
${HTS_LIB} -lm -lz -lcurl -llzma -lbz2
-lboost_program_options
-o bin/nimbus_call
build/read_provider.o: In function nimbus::ReadProvider(void*, bam1_t*)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:272: undefined reference to sam_read1'
build/read_provider.o: In function bam_hdr_destroy': /home/modenab/nimbus_project/samtools-1.10/htslib-1.10/htslib/sam.h:383: undefined reference to sam_hdr_destroy'
build/read_provider.o: In function nimbus::SequenceProvider::~SequenceProvider()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:90: undefined reference to hts_close'
build/read_provider.o: In function nimbus::SequenceProvider::initializePileup()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:151: undefined reference to bam_mplp_init'
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:152: undefined reference to bam_mplp_set_maxcnt' build/read_provider.o: In function nimbus::SequenceProvider::closePileup()':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:163: undefined reference to bam_mplp_destroy' build/read_provider.o: In function nimbus::SequenceProvider::next()':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:192: undefined reference to bam_mplp_auto' build/read_provider.o: In function nimbus::SequenceProvider::addSamFile(std::__cxx11::basic_string<char, std::char_traits, std::allocator >)':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:95: undefined reference to hts_open' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:96: undefined reference to sam_hdr_read'
build/alignment_functions.o: In function nimbus::ReadGroup[abi:cxx11](bam1_t const*)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:185: undefined reference to bam_aux_get'
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:189: undefined reference to bam_aux2Z' build/alignment_functions.o: In function nimbus::GetLabel(bam1_t const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:203: undefined reference to bam_aux_get' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:207: undefined reference to bam_aux2Z'
build/alignment_functions.o: In function nimbus::Amplicon[abi:cxx11](bam1_t const*)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:217: undefined reference to bam_aux_get'
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:219: undefined reference to bam_aux2Z' build/refsequence.o: In function nimbus::GenomeSequence::set(std::__cxx11::basic_string<char, std::char_traits, std::allocator >)':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/refsequence.cpp:21: undefined reference to fai_load' build/refsequence.o: In function nimbus::GenomeSequence::~GenomeSequence()':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/refsequence.cpp:27: undefined reference to fai_destroy' build/refsequence.o: In function nimbus::GenomeSequence::get[abi:cxx11](char const*, int, int)':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/refsequence.cpp:42: undefined reference to faidx_fetch_seq' build/refsequence.o: In function nimbus::GenomeSequence::get(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int, int)':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/refsequence.cpp:42: undefined reference to faidx_fetch_seq' build/mpileup.o: In function nimbus::Mpileup::initialize(nimbus::provider**, int)':
/home/modenab/nimbus_project/Nimbus/cplusplus/call/src/mpileup.cpp:45: undefined reference to bam_mplp_init' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/mpileup.cpp:46: undefined reference to bam_mplp_set_maxcnt'
build/mpileup.o: In function nimbus::Mpileup::next()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/mpileup.cpp:57: undefined reference to bam_mplp_auto'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:18: caller] Error 1
make[1]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/call'
make: *** [Makefile:19: call] Error 2

[RWWB]

Dear Brian, could you tell me which version of g++ you are using (g++ --version)? I want to try to recreate this issue on our own servers or desktop. Please give me a few days fix this issue. with kind regards, Rutger

…

On Tue, May 26, 2020 at 5:35 PM Brian Modena ***@***.***> wrote: Hi - I have a new RHEL 8 machine. While attempting to compile using "make" I get the following error messages. My search into the issue suggests it might be an issue with a mismatch in compilers. I am using the g++, as shown below. Thank you, Brian Modena ***@***.*** Nimbus]$ sudo make make -C cplusplus/trim make[1]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/trim' mkdir -p bin/ g++ build/adapter_trim.o -g -L/usr/lib64 -std=c++0x -pthread -Irwwb -Iinclude -lboost_program_options -o bin/nimbus_trim make[1]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/trim' make -C cplusplus/align make[1]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align' make -C lib/libnimbus make[2]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align/lib/libnimbus' mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AdapterTrim.cpp -o build/AdapterTrim.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Amplicon.cpp -o build/Amplicon.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Utils.cpp -o build/Utils.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/SAMrecord.cpp -o build/SAMrecord.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Read.cpp -o build/Read.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AmpliconIndex.cpp -o build/AmpliconIndex.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AmpliconAlignment.cpp -o build/AmpliconAlignment.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Alignment.cpp -o build/Alignment.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/_DNANode.cpp -o build/_DNANode.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/stdafx.cpp -o build/stdafx.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/io.cpp -o build/io.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/AlignmentBuilder.cpp -o build/AlignmentBuilder.o src/AlignmentBuilder.cpp: In member function ‘void Nimbus::AlnSet::delete_content()’: src/AlignmentBuilder.cpp:40:36: warning: deleting object of polymorphic class type ‘Nimbus::alignment::Alignment’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] if( f_alignment != NULL ) delete f_alignment ; ^~~~~~~~~~~ src/AlignmentBuilder.cpp:41:36: warning: deleting object of polymorphic class type ‘Nimbus::alignment::Alignment’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] if( r_alignment != NULL ) delete r_alignment ; ^~~~~~~~~~~ ar -cvq libnimbus.a build/AdapterTrim.o build/Amplicon.o build/Utils.o build/SAMrecord.o build/Read.o build/AmpliconIndex.o build/AmpliconAlignment.o build/Alignment.o build/_DNANode.o build/stdafx.o build/io.o build/AlignmentBuilder.o a - build/AdapterTrim.o a - build/Amplicon.o a - build/Utils.o a - build/SAMrecord.o a - build/Read.o a - build/AmpliconIndex.o a - build/AmpliconAlignment.o a - build/Alignment.o a - build/_DNANode.o a - build/stdafx.o a - build/io.o a - build/AlignmentBuilder.o rm -r build make[2]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align/lib/libnimbus' make -C lib/libthreadutils make[2]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align/lib/libthreadutils' mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/TQueue.cpp -o build/TQueue.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/stdafx.cpp -o build/stdafx.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude src/Signal.cpp -o build/Signal.o ar -cvq libthreadutils.a build/TQueue.o build/stdafx.o build/Signal.o a - build/TQueue.o a - build/stdafx.o a - build/Signal.o rm -r build make[2]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align/lib/libthreadutils' mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/preprocess.cpp -o build/preprocess.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/Worker.cpp -o build/Worker.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/Reader.cpp -o build/Reader.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/nimbus.cpp -o build/nimbus.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/nimbusheader.cpp -o build/nimbusheader.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/Writer.cpp -o build/Writer.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/opt.cpp -o build/opt.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/Manager.cpp -o build/Manager.o mkdir -p build g++ -c -g -Wall -O4 -std=c++0x -Iinclude -Ilib/libnimbus/include -Ilib/libthreadutils/include -pthread src/main.cpp -o build/main.o mkdir -p bin/ g++ build/preprocess.o build/Worker.o build/Reader.o build/nimbus.o build/nimbusheader.o build/Writer.o build/opt.o build/Manager.o build/main.o -g -L/usr/lib64 -std=c++0x -pthread -Iinclude -Llib/libnimbus -lnimbus -Ilib/libnimbus/include -Llib/libthreadutils -lthreadutils -Ilib/libthreadutils/include -o bin/nimbus_align rm -r build make[1]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/align' make -C cplusplus/call make[1]: Entering directory '/home/modenab/nimbus_project/Nimbus/cplusplus/call' mkdir -p bin/ g++ build/call.o build/read_provider.o build/alignment_functions.o build/mpileup.o build/aspects.o build/refsequence.o build/main.o build/sample.o build/cigar.o -g -L/usr/lib64 -std=c++0x -pthread ${HTS_LIB} -lm -lz -lcurl -llzma -lbz2 -lboost_program_options -o bin/nimbus_call build/read_provider.o: In function nimbus::ReadProvider(void*, bam1_t*)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:272: undefined reference to sam_read1' build/read_provider.o: In function bam_hdr_destroy': /home/modenab/nimbus_project/samtools-1.10/htslib-1.10/htslib/sam.h:383: undefined reference to sam_hdr_destroy' build/read_provider.o: In function nimbus::SequenceProvider::~SequenceProvider()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:90: undefined reference to hts_close' build/read_provider.o: In function nimbus::SequenceProvider::initializePileup()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:151: undefined reference to bam_mplp_init' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:152: undefined reference to bam_mplp_set_maxcnt' build/read_provider.o: In function nimbus::SequenceProvider::closePileup()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:163: undefined reference to bam_mplp_destroy' build/read_provider.o: In function nimbus::SequenceProvider::next()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:192: undefined reference to bam_mplp_auto' build/read_provider.o: In function nimbus::SequenceProvider::addSamFile(std::__cxx11::basic_string<char, std::char_traits, std::allocator >)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:95: undefined reference to hts_open' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/read_provider.cpp:96: undefined reference to sam_hdr_read' build/alignment_functions.o: In function nimbus::ReadGroup[abi:cxx11](bam1_t const*)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:185: undefined reference to bam_aux_get' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:189: undefined reference to bam_aux2Z' build/alignment_functions.o: In function nimbus::GetLabel(bam1_t const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:203: undefined reference to bam_aux_get' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:207: undefined reference to bam_aux2Z' build/alignment_functions.o: In function nimbus::Amplicon[abi:cxx11](bam1_t const*)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:217: undefined reference to bam_aux_get' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/alignment_functions.cpp:219: undefined reference to bam_aux2Z' build/refsequence.o: In function nimbus::GenomeSequence::set(std::__cxx11::basic_string<char, std::char_traits, std::allocator >)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/refsequence.cpp:21: undefined reference to fai_load' build/refsequence.o: In function nimbus::GenomeSequence::~GenomeSequence()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/refsequence.cpp:27: undefined reference to fai_destroy' build/refsequence.o: In function nimbus::GenomeSequence::get[abi:cxx11](char const*, int, int)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/refsequence.cpp:42: undefined reference to faidx_fetch_seq' build/refsequence.o: In function nimbus::GenomeSequence::get(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int, int)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/refsequence.cpp:42: undefined reference to faidx_fetch_seq' build/mpileup.o: In function nimbus::Mpileup::initialize(nimbus::*provider***, int)': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/mpileup.cpp:45: undefined reference to bam_mplp_init' /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/mpileup.cpp:46: undefined reference to bam_mplp_set_maxcnt' build/mpileup.o: In function nimbus::Mpileup::next()': /home/modenab/nimbus_project/Nimbus/cplusplus/call/src/mpileup.cpp:57: undefined reference to bam_mplp_auto' collect2: error: ld returned 1 exit status make[1]: *** [Makefile:18: caller] Error 1 make[1]: Leaving directory '/home/modenab/nimbus_project/Nimbus/cplusplus/call' make: *** [Makefile:19: call] Error 2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#8>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZVF5AHDDVKGSRQP6C4RFDRTPOSPANCNFSM4NKON44Q> .

[modenab]

Thank you Rutger. See below:

[modenab@localhost Nimbus]$ g++ --version
g++ (GCC) 8.3.1 20191121 (Red Hat 8.3.1-5)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Best,
Brian